Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
☆250Feb 25, 2026Updated last week
Alternatives and similar repositories for treetime
Users that are interested in treetime are comparing it to the libraries listed below
Sorting:
- Ultrafast Sample Placement on Existing Trees☆139Feb 6, 2026Updated last month
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆213Aug 27, 2025Updated 6 months ago
- An updated pipeline for pangenome investigation☆345Jan 15, 2026Updated last month
- Estimating time trees from very large phylogenies☆28Jul 21, 2024Updated last year
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆325Apr 29, 2025Updated 10 months ago
- Create a tree using Mash distances☆184Oct 24, 2023Updated 2 years ago
- The ARTIC fieldbioinformatics pipeline☆130Feb 24, 2026Updated last week
- RAxML Next Generation: faster, easier-to-use and more flexible☆452Updated this week
- A collection of documented examples using TreeTime☆22Jul 30, 2019Updated 6 years ago
- snipit: summarise snps relative to your reference sequence☆167Jan 13, 2026Updated last month
- Finds SNP sites from a multi-FASTA alignment file☆275Dec 16, 2020Updated 5 years ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆120May 21, 2024Updated last year
- A tool for exploring large trees in the browser☆123Feb 4, 2026Updated last month
- Scalable relaxed clock phylogenetic dating☆28Sep 3, 2025Updated 6 months ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆29Jul 18, 2025Updated 7 months ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 8 months ago
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆122Jan 20, 2026Updated last month
- Rapid haploid variant calling and core genome alignment☆569Dec 12, 2025Updated 2 months ago
- Parallel/Homoplasic SNP Finder☆21May 3, 2023Updated 2 years ago
- Synteny and Rearrangement Identifier☆448Apr 29, 2025Updated 10 months ago
- Processing pipeline for pan-genome visulization and exploration☆144Oct 9, 2023Updated 2 years ago
- Rapid determination of appropriate reference genomes.☆100Jan 22, 2025Updated last year
- Reorients assembled microbial sequences☆135Aug 21, 2025Updated 6 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- Graph-based assembly phasing☆91Nov 25, 2025Updated 3 months ago
- Efficient phylogenetic tree inference for massive taxonomic datasets☆141Apr 6, 2025Updated 11 months ago
- A toolbox for pangenome analysis and threshold evaluation.☆99Jul 8, 2022Updated 3 years ago
- Split k-mer analysis – version 2☆104Jan 29, 2026Updated last month
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆607Feb 18, 2026Updated 2 weeks ago
- SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity☆13Aug 14, 2023Updated 2 years ago
- Quality control for phylogenetic analyses☆13Updated this week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10Feb 27, 2026Updated last week
- Pipeline components for real-time phylodynamic analysis☆275Updated this week
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆255Dec 13, 2025Updated 2 months ago
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Bifrost graph gene caller.☆98Jan 20, 2026Updated last month
- Gene cluster comparison figure generator☆637Dec 22, 2025Updated 2 months ago
- Visualization of the pan-genome output by panX☆67Jun 16, 2025Updated 8 months ago